DIALS 3.10.0

2022-06-09:

Features

• dials.export: MTZ files are now exported with geometry in the Cambridge frame (#2054), and conformance with the latest mmcif standards (#2078).
• dials.index: Performance improvements for serial indexing. (#2035)
• dials.merge: New implementation of the French & Wilson (1978) algorithm, which makes the procedure robust against the presence of very negative intensities. (#2100)
• dials.powder_calibrate: Add detector distance calibration. (#2075)
• dials.refine: Reduced memory requirements and improved running time (#1427, #2022). A new separate_images option performs outlier rejection on each image independently. (#2036)
• dials.scale: Allow use of a pdb model to calculate target intensities for scaling (target_model=). (#2053)
• xia2: dev.xia2.ssx: Add first part of a developmental ssx processing pipeline (data integration) (xia2/xia2#670)

Bugfixes

• dials.reindex: Fail with a helpful error message when attempting to reindex to a left-handed cell. (#1779)
• dials.scale: If scaling against a target, do targeted outlier rejection. (#2052)
• dials.show: Avoid crash when an experiment does not have an imageset. (#2056)
• dials.image_viewer: Fixed user setting for show_beam_center= being overridden (#2103). Properly handle the n_iqr value for radial_profile thresholding (#2116).
• dials.refine_bravais_settings: Ensure that the reported reindexing operators correctly map the input symmetry to the given Bravais settings, regardless of whether the input symmetry was a primitive or non-primitive setting (#2105)
• dials.scale: Respect user supplied high resolution limit in summary table. (#2118)
• dials.export: Fix crash for exporting ssx data (#2126)
• dxtbx: Fixed Panel.projection_2d_ not being serialized. (cctbx/dxtbx#509)
• dxtbx: Fix dxtbx.image_average for raster scans. (cctbx/dxtbx#522)
• xia2: Fix cases where NeXus files not following the Eiger conventions (``/entry/data/data_[nnnn]```) were ignored. (xia2/xia2#672)
• xia2: Fix bug in pipeline=dials where the working directory contains the letters "mtz". (xia2/xia2#674)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.

DIALS 3.9.2

2022-05-09:

• dials.show: Fix display of unknown vector columns. (#2048)
• dxtbx: FormatCBFFullPilatus: Handle detector information better in cases of multiple or missing panels. (cctbx/dxtbx#508)
• dxtbx: Remove check for beam/normalization orthogonality in Beam.rotate_around_origin. This could stop processing of older, incorrectly configured data. (cctbx/dxtbx#510)
• dxtbx: Correct a unicode error reading Bruker .sfrm files. With thanks to Dennis Brookner for this change. (cctbx/dxtbx#518)

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to cctbx or xia2 in this release.

DIALS 3.8.4 LTS

2022-04-01:

• dials.scale: Fix crash when a dataset is filtered out during the scaling process (issue #2045). (#2045)
• dxtbx: FormatNXmxI19_2: Allow data from beamline I19-2 at Diamond Light Source to be processed with optional masking of the beamline's standard diamond anvil pressure cell with a 76° aperture. (cctbx/dxtbx#481)
• cctbx: Allow usage of GUI interfaces when configuring on MacOS.

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to xia2 in this release.

DIALS 3.9.1

2022-03-31:

• dials.scale: Fix crash when a dataset is filtered out during the scaling process (issue #2045). (#2045)
• dxtbx: Windows support for the CMake build. (cctbx/dxtbx#507)
• cctbx: Allow usage of GUI interfaces when configuring on MacOS.

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to xia2 in this release.

DIALS 3.9.0

2022-03-14:

Features

• dials.background now writes to a log file. (#1948)
• dials.export: Add SHELX .hkl file output. (#1925)
• dials.cluster_unit_cell: Add option output.clusters=True/False to generate output for each clustersplit at a given threshold. (#1950)
• dials.reindex: Allow reindexing using multi-crystal reference data files. (#1977)
• xia2.delta_cc_half: Add overall CC½, plus a completeness column to the table. (xia2/xia2#645)
• Add experimental dev.dials.ssx_integrate script for profile modelling and integration of SSX data, including ellipsoid profile modelling. (#1974)
• For data reduction programs, allow exclude_images= to take a single multi-sweep command. (#1996)
• Add flex.reflection_table.match_by_hkle method, to match reflections between tables that have the same miller index and entering flags. (#1951)
• Add flex.reflection_table.concat method, to concatenate reflection tables and handle experiment id remapping (#1994)
• dxtbx: Beam flux is now written to, and read from, CBF files. (cctbx/dxtbx#493)
• Use the perceptually uniform colour map Viridis in plotly plots. Thanks to Ammaar Saeed (ammsa23) for this change. (#2026)

And several features for electron diffraction data processing:

• dials.export: Add PETS 2 exporting, for processing electron diffraction data. (#2014)
• dials.find_spots: Added new spotfinder.threshold=radial_profile threshold algorithm. This calculates an average background in 2θ shells, and identifies peak pixels above the background. Particularly appropriate for cases such as electron diffraction images. (#2009)
• New tool - dials.powder_calibrate to help calibrate the geometry of an electron powder pattern. (#2016)

Bugfixes

• dials.scale: Fixes to properly handle partiality of ssx data (#1965)
• Avoid using the uuid module, to avoid mpi errors on Python 3.8. (#2000)
• dials.refine: Avoid spike in memory usage while saving reflections. (#2024)
• dxtbx: Reduce, in some cases drastically, memory usage of ImageSet objects. (cctbx/dxtbx#438)
• dxtbx: FormatNXmxI19_2: Allow data from beamline I19-2 at Diamond Light Source to be processed with masking of the beamline's diamond anvil pressure cell. (cctbx/dxtbx#481)
• dxtbx: The Beam object constructor no longer discards "transmission" and "flux". (cctbx/dxtbx#488)
• dxtbx: Fix wavelength bug in FormatXTC for older datasets (cctbx/dxtbx#490)
• xia2.multiplex: Allow processing imported mtz when imageset is absent. (xia2/xia2#641)
• xia2: Avoid hanging on a call to pointless to get version information. (xia2/xia2#651)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.

DIALS 3.8.3 LTS

2022-02-22:

• dials.cosym: Fix crash for edge case of a full dataset being excluded by the resolution filter (#1993)
• dials.two_theta_refine: Fix crash if running on scaled data with exclude_datasets=. (#2006)
• Fix downloads failing on MacOS with "426 Upgrade Required" (#2012)
• dxtbx: FormatNXmx: Open nexus files in SWMR mode. (cctbx/dxtbx#478)

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to cctbx or xia2 in this release.

DIALS 3.8.2 LTS

2022-02-07:

• dxtbx.dlsnxs2cbf: Provide more general support for correctly formatted NXmx-flavoured NeXus data. Previously, only a very limited subset of experiment geometries and data formats were supported. (cctbx/dxtbx#453)
• dxtbx: More robustly handle different ways of recording single-value NXmx detector metadata. (cctbx/dxtbx#460)
• dxtbx: Fix dxtbx.plot_detector_models running on newer matplotlib versions. (cctbx/dxtbx#475)

For a more complete list of changes and fixed bugs check the dxtbx changelog.

There are no changes to cctbx, dials or xia2 in this release.

DIALS 3.8.1 LTS

2022-01-25:

• It is now possible to explicitly bootstrap DIALS 3.8 with all supported python versions. (#1988)
• dials.refine: Fix crash from recording of parameter correlations in history.json. (#1923)
• Correct reporting of phi angle in scan-varying model plots. (#1929)
• dials.sequence_to_stills: correct error in the crystal model for scans that do not start from image 1. (#1933)
• dials.show: only show format class if meaningful (i.e. not Format or FormatMultiImage). (#1981)
• Update some Cosym and resolution-related PHIL descriptions. (#1969)
• xia2.multiplex: Add, and update, PHIL parameter descriptions. (xia2/xia2#644)
• dxtbx: Updated bad pixel mask for DLS I23 PILATUS 12M for 2022 run 1. (cctbx/dxtbx#469)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.

There are no changes to cctbx in this release.

DIALS 3.8.0 LTS

2022-01-11:

This is an LTS release and support will continue until the end of the year. This is also the last release to support Python 3.7.

Features

• dials.indexed_as_integrated: New tool to make an indexed reflection file look as if it were summation integrated. Allows symmetry and scaling analysis on indexed data, for very rapid feedback data processing. (#1912)
• All command line programs now allow passing -h argument multiple times to increase verbosity. (#1920)
• Add experimental dev.dials.ssx_index script to index a block of ssx data. (#1955)
• Add aliases dials.rlv for dials.reciprocal_lattice_viewer, and dials.rbs for dials.refine_bravais_settings. (#1959)
• xia2.multiplex: Extend available deltacchalf filtering options to match those in dials.scale. (xia2/xia2#631)
• xia2.compare_merging_stats called with latex=True now includes cc-anom. (xia2/xia2#633)

Bugfixes

• dials.import: Support arbitrary P1 known unit cells settings. (#1880)
• Better handle cases of missing partiality data in reflection files. (#1911)
• dials.scale: Add missing "expids_and_image_ranges" information to the json output. This is required for some of the plots in dials.report output. (#1913)
• dials.check_indexing_symmetry: correctly handle d_max= parameter if left at default value when d_min= set. (#1957)
• dials.image_viewer: Fix plotting of max and min absorption due to Kapton tape corrections. (#1962)
• dxtbx: Fix an arithmetic mistake in dxtbx.model.Goniometer.rotate_around_origin, which was mangling the addition of a new rotation to the goniostat rotation operator :math:\mathbf{R}. (cctbx/dxtbx#451)
• dxtbx: Correct pedestal handling for simulated images from simtbx. (cctbx/dxtbx#456)
• dxtbx: Ensure FormatTIFF only understands images with the expected basic TIFF header. (cctbx/dxtbx#457)
• xia2.compute_merging_stats: Avoid warning in output. (xia2/xia2#636)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.

DIALS 3.7.1

2021-11-17:

• Fix frozen bootstrap package list to account for backported change in conda-forge dependencies (ef0d20d)
• dials.export: No longer allow (erroneous) MTZ export for multiple experiments with multiple space groups. (#1915)
• dials.export: No longer fails for XDS_ASCII and SADABS export with intensity=auto. (#1926)
• dials.report: Fix broken json output option. Include more graphs in json output. (#1932)
• xia2.multiplex: Include additional graphs in json output (xia2/xia2#637)

For a more complete list of changes and fixed bugs check the dials and xia2 changelogs.

There are no changes to cctbx or dxtbx in this release.